SUMMARY Thousands of long intervening non-coding RNAs (lincRNAs) have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs, we used chromatin marks, poly(A)-site mapping and RNA-Seq data, to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs, only 29 had detectable sequence similarity with putative mammalian orthologs, typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without detectable sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation.

Poly(A) tails enhance the stability and translation of most eukaryotic mRNAs, but difficulties in globally measuring poly(A)-tail lengths have impeded greater understanding of poly(A)-tail function. Here, we describe poly(A)-tail length profiling by sequencing (PAL-seq) and apply it to measure tail lengths of millions of individual RNAs isolated from yeasts, cell lines, Arabidopsis leaves, mouse liver, and zebrafish and frog embryos. Poly(A)-tail lengths were conserved between orthologous mRNAs, with mRNAs encoding ribosomal proteins and other “housekeeping” proteins tending to have shorter tails. As expected, tail lengths were coupled to translational efficiency in early zebrafish and frog embryos. However, this strong coupling diminished at gastrulation and was absent in non-embryonic samples, indicating a rapid developmental switch in the nature of translational control. This switch complements an earlier switch to zygotic transcriptional control and explains why the predominant effect of microRNA-mediated deadenylation concurrently shifts from translational repression to mRNA destabilization.

We have analyzed the kinetics of accumulation of each of the individual core histone mRNAs throughout the HeLa cell cycle in cells synchronized by sequential thymidine and aphidicolin treatments. These analyses showed that during the S phase there was a 15-fold increase in the levels of histone mRNAs and that this resulted from both an increased rate of synthesis and a lengthening of the half-life of histone mRNAs. A comparison of the kinetics of accumulation of histone mRNA in the total cellular and nuclear RNA populations suggested an increased transcription rate through the S phase. Within 30 min after the inhibition of DNA synthesis in mid-S phase, the steady-state concentration and the rate of synthesis of histone mRNA each declined to their non-S-phase levels. Reactivation of histone mRNA accumulation could occur even after an extended mid-Sphase block in DNA synthesis. These results suggest that the mechanisms responsible for histone mRNA synthesis are not restricted to the Gl/S boundary of the HeLa cell cycle, but can operate whenever DNA synthesis is occurring.